diff --git a/rhodecode/apps/admin/views/settings.py b/rhodecode/apps/admin/views/settings.py
--- a/rhodecode/apps/admin/views/settings.py
+++ b/rhodecode/apps/admin/views/settings.py
@@ -47,6 +47,7 @@ from rhodecode.model.db import RhodeCode
 from rhodecode.model.forms import (ApplicationSettingsForm,
     ApplicationUiSettingsForm, ApplicationVisualisationForm,
     LabsSettingsForm, IssueTrackerPatternsForm)
+from rhodecode.model.permission import PermissionModel
 from rhodecode.model.repo_group import RepoGroupModel
 
 from rhodecode.model.scm import ScmModel
@@ -253,8 +254,7 @@ class AdminSettingsView(BaseAppView):
         c.active = 'mapping'
         rm_obsolete = self.request.POST.get('destroy', False)
         invalidate_cache = self.request.POST.get('invalidate', False)
-        log.debug(
-            'rescanning repo location with destroy obsolete=%s', rm_obsolete)
+        log.debug('rescanning repo location with destroy obsolete=%s', rm_obsolete)
 
         if invalidate_cache:
             log.debug('invalidating all repositories cache')
@@ -263,6 +263,8 @@ class AdminSettingsView(BaseAppView):
 
         filesystem_repos = ScmModel().repo_scan()
         added, removed = repo2db_mapper(filesystem_repos, rm_obsolete)
+        PermissionModel().trigger_permission_flush()
+
         _repr = lambda l: ', '.join(map(safe_unicode, l)) or '-'
         h.flash(_('Repositories successfully '
                   'rescanned added: %s ; removed: %s') %
diff --git a/rhodecode/model/permission.py b/rhodecode/model/permission.py
--- a/rhodecode/model/permission.py
+++ b/rhodecode/model/permission.py
@@ -577,7 +577,8 @@ class PermissionModel(BaseModel):
                 user_group_write_permissions[p.users_group_id] = p
         return user_group_write_permissions
 
-    def trigger_permission_flush(self, affected_user_ids):
+    def trigger_permission_flush(self, affected_user_ids=None):
+        affected_user_ids or User.get_all_user_ids()
         events.trigger(events.UserPermissionsChange(affected_user_ids))
 
     def flush_user_permission_caches(self, changes, affected_user_ids=None):